Functional Magnetic Resonance Imaging (fMRI) Methods

Question 1

What is PET?

Answer 1

Positron Emission Tomography.

Question 2

Define PET.

Answer 2

PET is a process which involves administering a radioactive isotope to the patient (e.g. oxygen-15), thereby exposing the patient to a significant amount of ionizing radiation.

Question 3

Define fMRI and a brief comparative overview.

Answer 3

fMRI (Functional Magnetic Resonance Imaging) is an imaging method that has become increasingly common as it involves no radiation, as opposed to PET.

Question 4

Describe the process of using a fMRI.

Answer 4

• Participant is placed on the bed and moved into the magnet
• Experiments can be controlled from outside the scanner room
• No metal is to be taken into the scanner room
• Participants can see a projection via mirrors mounted on the head coil
• Responses can be given via scanner-compatible keys, joystick, touchpad
• The head coil is used to send radio frequency pulses and also functions as a receiver
• Head position is fixed to avoid any movement

Question 5

What does the MRI capture?

Answer 5

The structure of the brain.

Question 6

True or False: More than 70% of the brain consists of water.

Answer 6

True.

Question 7

Provide a brief overview regarding precession frequency.

Answer 7

Hydrogen atoms (H+ protons) can be thought as small bar magnets, ‘precessing’ like a spinning top about an axis

• Random spin directions of protons can be aligned parallel to or anti-parallel to an externally applied very strong magnetic field in the MRI scanner
• However, they are not perfectly aligned and they also not static, but they still keep precessing in a random fashion.
• The precession frequency of proton depends on the strength of the magnetic field

Question 8

Describe magnetization.

Answer 8

• The axis along which the magnetization is build up in the scanner i called the Z-axis
• However, the magnetisation along the Z-axis can’t be measured
• We need to tilt the magnetisation vector
• a radio frequency (RF) pulse is applied perpendicular to magnetic field
• Its amplitude is matching the precession frequency of the protons: the frequency with which the protons precess about their axis
• The RF pulse causes the protons to absorb energy. And this has 2 additional effects:
  a) it tilts the magnetisation vector to the transversal plane
  b) it aligns the precession of the spins, which means that the protons’ rotations are ‘in phase’

Question 9

From magnetization, continue explaining MRI.

Answer 9

• The transversely rotating magnetization vector can then be recorded as a signal: The head coil is used to send the RF pulses, but it is also the receiver
• The trick is, however, to now switch off the RF pulse
• After switching off the RF pulse the transversal magnetisation decays- the protons emit the excess energy
• They also lose phase coherence very quickly
• The effect is that the transversal magnetization disappears and the longitudinal magnetization is re-established
• These processes are called ‘relaxation’
• The summed effect of many protons doing this can be measured during the relaxation phase
• longitudinal/spin lattice relaxation
• transversal/spin-spin relaxation

Question 10

Describe some caveats/limitations regarding MRI utilisation.

Answer 10

• The transversal magnetization decays with different speeds depending on the tissue
• One of the reasons for this is differences in the density of protons: They lose coherence because they will be influenced by other protons in their environment
• The signals from different protons will get out of phase with each other and begin to cancel each other out
• Structural brain image depends on when signal is recorded during this process

Question 11

Describe why it is necessary to reconstruct brain images.

Answer 11

• In order to get separate measurements from different locations in the brain, we need to decide where exactly our signal comes from
• This means, we cannot excite the entire brain with RF pulses at the same time because then we could not reconstruct the source of the measured signal
• For this, we use a trick: We know that protons will absorb energy from RF pulses only when the frequency of the RF pulse matches the proton’s precession (also called ‘resonance’) frequency
• Thus, by causing the magnetic field to vary linearly, we can cause the resonance frequency to vary throughout the brain- this can be achieved by using gradients.
• An RF pulse of a specific frequency will now only excite one slice of the brain- precisely the slice where the resonance frequency of the protons matches the frequency of the RF pulse.

Question 12

What is the first step in reconstructing brain images?

Answer 12

• The first step is therefore to divide the brain into ‘slices.’ We can now vary the gradient field along the z-axis and know that different slices were exposed t different strengths: This is the ‘slicing selecting gradient’
• Thus, if different protons are in different magnetic fields, their precession frequencies will be different. This means, only one slice will be excited at a time using a specific RF pulse, because for the others, the precession frequency will not be matched.
• By exciting one slice at a time, we get the z-coordinate of all resulting signals

Question 13

What is the second step in reconstructing brain images?

Answer 13

• Now, we can use a second gradient to change the magnetic field within this slice: during readout, we vary the gradient along the y-axis.
• This means, protons in each slice also have different precession frequencies
• This gradient is therefore called ‘frequency encoding gradient’
• This gives us the y-coordinates of the measured signal

Question 14

What is the third step in reconstructing brain images?

Answer 14

• Finally, very briefly using a gradient along the x-axis causes protons to ‘speed up’ their precession according to the strength of the magnetic field for a very short time
• When switching off this gradient, all protons are all back to the same precessing frequency, but they are ‘out of phase’ with each other
• This gradient is therefore called ‘phase encoding gradient’
• By measuring the phase signal, we now also get the x-coordinate of the resulting signal

Question 15

Provide an overview of the RBI process.

Answer 15

• Now that we know precisely what we have done to the protons at each location in space, we can use a technique called Fourier transformation, to reconstruct the entire space
• This process- setting the gradients, sending the RF pulses, switching them off and measuring signal at precisely the right moment- takes some tim, and we also measure each slice separately, meaning that it takes time to measure the entire brain once
• We can measure slices in ascending order, descending order, or interleaved, until we have a full 3D image of the brain
• Usually, measuring one full 3D image of the brain takes 1-3 seconds (~2s is standard)